Photoreactivation of killing in Streptomyces. II. Kinetics of formation and photolysis of pyrimidine dimers and adducts in S. coelicolor and S. griseus PHR-1

Abstract— A pyrimidine adduct, 6-4‘-[pyrimidine-2’-one] thymine (PO-T)?, observed in DNA hydrolysates of 254-nm ultraviolet (u.v.) irradiated conidia of Streptomyces coelicolor, increases linearly with u.v. dose up to 2 × 10⁵ ergs/mm². Yields of thymine dimer (T○) and uracil-thymine dimer (U○) level off at much lower doses. Initial relative rates of formation of these u.v. photoproducts are: 1:1.3:4.8 for PO-T, T○ and U○, respectively. Similar results were obtained with a Streptomyces griseus mutant, PHR-1. An equation is derived to estimate the ratio of the amount of PO-T to the total amount of thymine-derived photoproducts at low (biological) u.v. doses. The observed PO-T fractions compare well with the calculated values. Rapid photolysis of the precursor of PO-T was observed by post-u. v. treatment at 313 nm of conidia of S. coelicolor and of S. griseus PHR-1. The photolysis was much slower at 365 nm and did not occur at all at 405 nm. Pyrimidine dimers were not appreciably affected by post-u. v. treatment at the above wavelengths in these Streptomyces strains. Both of these strains are phenotypically photoreactivation-deficient, and the present results indicate that they do not possess active photoreactivating enzyme. In earlier papers[3,4,5], the pyrimidine adduct found in acid hydrolysates of DNA was loosely referred to as “uracil-thymine adduct (U-T adduct)”. Such terminology is not strictly correct. The pyrimidine adduct in acid hydrolysates is PO-T (sometimes called P₂B), which could theoretically result from removal of ammonia from a C-T adduct or removal of water from a U-T adduct (see [6]).     

Photoreactivation of killing in Streptomyces: action spectra and kinetic studies

Abstract— An action spectrum was obtained for photoreactivation of killing (PR) of Streptomyces griseus conidia. This spectrum shows a major peak around 436 nm, originally observed by A. Kelner, and a secondary peak at 313 nm not previously reported. The rate of PR shows a strong dependence upon temperature and dose rate of the PR light at 436 nm, but this decreases to only a slight dependence upon these parameters at 313 nm. These findings suggested that PR at 436 nm in this organism is of the usual photoenzymatic type, but that PR at 313 nm might be of a different kind. A mutant (PHR-1) of S. griseus was found that shows only a narrow range of PR (roughly 310–400 nm) with a single peak at 313 nm. The PR efficiency was lower than for wild type and the PR sector not greater than one-half that of wild type. This PR shows no temperature dependence. Essentially similar behavior was observed with wild-type Streptomyces coelicolor. These findings show that at least some of the PR at 313 nm is a separable phenomenon. It is therefore unlikely to involve a mechanism identical to that at 436 nm. The nature of PR at 313 nm in Streptomyces is not known. If it is enzymatic, it is remarkable in having little or no dependence upon temperature and dose rate. Absence of photoprotection and liquid-holding recovery indicate that it is not indirect PR. Some of it (that part exhibited by S. griseus PHR-1 and S. coelicolor) might result from a direct photochemical action on DNA.     

Photoreactivation of RNA in UV-irradiated insect eggs (Smittia sp., Chironomidae, Diptera) I. Photosensitized production and light-dependent disappearance of pyrimidine dimers

Abstract. Irradiation of Smittia eggs with UV during intravitelline cleavage causes the formation of pyrimidine dimers in the (largely ribosomal) RNA of the eggs. The yield of dimers is wavelength-dependent in a way that strongly suggests the involvement of photosensitizing egg components. Illumination of UV-irradiated eggs with light (380 or 400 nm) causes both photoreactivation of the eggs and mono-merization of the pyrimidine dimers in their RNA. The photoreactivable sector of the biological damage is correlated with the amount of pyrimidine dimers present in the RNA after inactivation of the eggs with UV of different wavelengths. The data are regarded as the first direct evidence that the photoreactivation of a eukaryotic organism is correlated with the light-dependent (and apparently enzymatic) monomerization of pyrimidine dimers in RNA.     

Near-U.V. photolysis of pyrimidine heteroadducts in E. coli DNA

Abstract— The cytosine-thymine precursor of the U–T adduct is not subject to enzymatic photoreactivation, but can be eliminated directly from u.v.-irradiated E. coli DNA by exposure to wavelengths around 313 nm.     

Calculation of vibrational spectra of linear tetrapyrroles. 3. Hydrogen-bonded hexamethylpyrromethene dimers

The structure and vibrational spectra of hexamethylpyrromethene (HMPM) have been investigated by X-ray crystallography, IR and Raman spectroscopies, and density functional theory calculations. HMPM crystallizes in the form of dimers, which are held together by bifurcated N-H(...N)(2) hydrogen bonds, involving one intramolecular and one intermolecular N-H...N interaction. The monomers are essentially planar, and the mean planes of the monomers lie approximately perpendicular to one another, so that the four N atoms in the dimer form a distorted tetrahedron. The structure of the HMPM dimer is well-reproduced by B3LYP/6-31G calculations. A comparison of the calculated geometry of the dimer with that of the monomer reveals only small changes in the N-H...N entity and the methine bridge angles upon dimerization. These are a result of weakening of the intramolecular N-H...N hydrogen bond and the formation of a more linear N-H...N intermolecular hydrogen bond. Using an empirical relation between the shift of the N-H stretching frequency of pyrrole and the enthalpy of adduct formation with bases [Nozari, M. S.; Drago, R. S. J. Am. Chem. Soc. 1970, 92, 7086-7090], estimates of the strength of the intra- and intermolecular hydrogen bonds are obtained. IR and Raman spectroscopies of HMPM and its isotopomers deuterated at the pyrrolic nitrogen atom and at the methine bridge reveal that the molecule is monomeric in nonpolar organic solvents but dimeric in a solid Ar matrix and in KBr pellets. The matrix IR spectra show a splitting of vibrational modes for the dimer, particularly those involving the N-H coordinates. Due to intrinsic deficiencies of the B3LYP/6-31G approximation, a satisfactory reproduction of these modes of the monomeric and dimeric HMPM requires specific adjustments of the NH scaling factors for the calculated force constants and, in the case of the NH out-of-plane modes of HMPM dimers, also of intra- and intermolecular coupling constants. This parametrization does not significantly affect the other calculated modes, which in general reveal a very good agreement with the experimental data.     

A triplet mechanism for the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA

The reaction pathways for the photochemical formation of cyclobutane thymine dimers in DNA are explored using hybrid density functional theory techniques. It is concluded that the thymine-thymine [2 + 2] cycloaddition displays favorable energy barriers and reaction energies in both the triplet and the singlet excited states. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction. The triplet mechanism is thus completely different from the concerted singlet state cycloaddition processes. The key geometric features and electron spin densities are also discussed. Bulk solvation has a major effect by reducing the barriers and increasing the diradical stabilities. The present results provide a rationale for the faster cycloreaction observed in the singlet excited states than in the triplet excited states.     

Diels-alder adducts of a spirocyclopentenotriazoloazodienophile. Assignment of their 1H and 13C NMR spectra

1-Phenyl-cyclopenteno[1,2-d]-1,2,3-rriazolo-5-spiro-4′-[perhydropyrazolino-3′,5′-dione] (5) afforded in situ, by oxidation with lead tetraacetate, the corresponding cyclopentenotriazolo-spiropyrazolodione 6 , which was trapped with dienes giving the hetero-Diels-Alder adducts 10–12 in good yields. The Diels-Alder reactions were examined on the basis of AM1 MO calculations. Total assignment of the ¹H- and ¹³C-nmr chemical shifts as well as the relative configuration of these adducts was accomplished with the help of 2D (¹H-¹H COSY, ¹H -¹ H NOESY, ¹H-¹³C XHCORR, ¹H-¹³C COLOC) and NOE difference spectroscopy. The structures of compounds 11a and 11b were also examined by molecular modeling.     

UV spectra of benzene isotopomers and dimers in helium nanodroplets

We report spectra of various benzene isotopomers and their dimers in helium nanodroplets in the region of the first Herzberg-Teller allowed vibronic transition 6(0)(1) (1)B(2u)<--(1)A(1g) (the A(0) (0) transition) at approximately 260 nm. Excitation spectra have been recorded using both beam depletion detection and laser-induced fluorescence. Unlike for many larger aromatic molecules, the monomer spectra consist of a single "zero-phonon" line, blueshifted by approximately 30 cm(-1) from the gas phase position. Rotational band simulations show that the moments of inertia of C(6)H(6) in the nanodroplets are at least six-times larger than in the gas phase. The dimer spectra present the same vibronic fine structure (though modestly compressed) as previously observed in the gas phase. The fluorescence lifetime and quantum yield of the dimer are found to be equal to those of the monomer, implying substantial inhibition of excimer formation in the dimer in helium.     

Infrared spectra of matrix isolated and solid ethylene. Formation of ethylene dimers

Spectra of matrices with ethylene/argon ratios from 1/1 to 1/999 and a 1/24 ethylene/xenon matrix have been recorded in the temperature range 15–105 K. From relative i.r. intensities, frequency shifts and statistical calculations, the data are interpreted in terms of a monomer → dimer → aggregate → crystal scheme. It is proposed that the dimer, (C₂H₄)₂, has D_2d symmetry with a structure determined by quadruple hydrogen bonding and hydrogen-hydrogen repulsion. A method is described for calculation of the vibrational splitting due to interactions between the dimer molecular constituents.Solid ethylene has been studied between 15 and 85K. A transformation between two crystalline phases is characterized.     

Absorption spectra and photolysis of methyl peroxide in liquid and frozen water

Methyl peroxide (CH(3)OOH) is commonly found in atmospheric waters and ices in significant concentrations. It is the simplest organic peroxide and an important precursor to hydroxyl radical. Many studies have examined the photochemical behavior of gaseous CH(3)OOH; however, the photochemistry of liquid and frozen water solutions is poorly understood. We present a series of experiments and theoretical calculations designed to elucidate the photochemical behavior of CH(3)OOH dissolved in liquid water and ice over a range of temperatures. The molar extinction coefficients of aqueous CH(3)OOH are different from the gas phase, and they do not change upon freezing. Between -12 and 43 °C, the quantum yield of CH(3)OOH photolysis is described by the following equation: Φ(T) = exp((-2175 ± 448)1/T) + 7.66 ± 1.56). We use on-the-fly ab initio molecular dynamics simulations to model structures and absorption spectra of a bare CH(3)OOH molecule and a CH(3)OOH molecule immersed inside 20 water molecules at 50, 200, and 220 K. The simulations predict large sensitivity in the absorption spectrum of CH(3)OOH to temperature, with the spectrum narrowing and shifting to the blue under cryogenic conditions because of constrained dihedral motion around the O-O bond. The shift in the absorption spectrum is not observed in the experiment when the CH(3)OOH solution is frozen suggesting that CH(3)OOH remains in a liquid layer between the ice grains. Using the extinction coefficients and photolysis quantum yields obtained in this work, we show that under conditions with low temperatures, in the presence of clouds with a high liquid-water content and large solar zenith angles, the loss of CH(3)OOH by aqueous photolysis is responsible for up to 20% of the total loss of CH(3)OOH due to photolysis. Gas phase photolysis of CH(3)OOH dominates under all other conditions.     

Photoreactivation of cyclobutane dimers and (6-4) photoproducts in the epidermis of the marsupial, Monodelphis domestica

Radioimmunoassays were used to investigate the repair of cyclobutane pyrimidine dimers and pyrimidine (6-4)pyrimidone photoproducts ((6-4] photoproducts) in the epidermis of the South American opossum, Monodelphis domestica. In the absence of photoreactivating light, both types of photodamage were excised with similar kinetics, 50% of the damage remaining 8 h after UV irradiation in vivo. Exposure of UV-irradiated skin to photoreactivating light resulted in removal of most of the cyclobutane dimers and an enhanced rate of (6-4) photoproduct repair. Photoenhanced excision repair of non-dimer damage increases the range of biologically effective lesions removed by in vivo photoreactivation.     

N.m.r. spectra of prostaglandin metabolites and precursors and of related pyrazoline adducts

The ¹³C n.m.r. spectra of the major human urinary metabolite of prostaglandin PGE₂ and PGE₁ are discussed together with some unsaturated precursors. Δ-2-Pyrazolines, formed by addition of diazomethane to the 11-oxo dienediones in this series, were identified by ¹³C and ¹H n.m.r. and by other physical methods.